Japan is facing one of the world's biggest nuclear crises as a team of engineers struggles to regain control of the Fukushima plant following another explosion and a fire that caused radiation to rise to harmful levels.

Amid growing fears that the situation is heading for catastrophe, up to 70 technicians are still battling to cool reactors at the Fukushima Daiichi facility. Non-essential personnel have been ordered to leave and the Kyodo news agency reported that radiation levels have become too high for staff to remain in control rooms.

The government has already called in international help in tackling the spiralling crisis.

Officials are now concerned about all six reactors at the site, and are considering using helicopters to try to drop cold water on a boiling rooftop storage pond for spent uranium fuel rods. The rods are still radioactive and potentially as hot and dangerous as the fuel rods inside the reactors if not kept in water.

Early on Tuesday, the power plant in the country's stricken north-east was rocked by an explosion at the No 2 reactor, the third blast at the site in four days. That was followed by a fire that broke out at the No 4 reactor unit, which appeared to be the cause of today's radiation leaks. There are now concerns about the storage ponds at reactors 5 and 6.

Reactor No 4 was shut down for maintenance before the earthquake, but its spent fuel rods are stored in a pool at the site. The fire on Tuesday was extinguished, but Kyodo reported that the pool was subsequently boiling, with the water level falling. If the water boils off there is a risk that the fuel could catch fire, sending a plume of radiation directly into the atmosphere.

Radiation levels at one location at the site reached 400 millisieverts (mSv) an hour after the fire – four times the level that can lead to cancer – Yukio Edano, the chief cabinet secretary, said. But levels had lowered dramatically by the end of the day, according to the International Atomic Energy Authority (IAEA).

According to experts, engineers are now locked in a desperate fight to prevent all three reactors overheating. The risk appears highest at reactor No 2, where fuel rods were repeatedly exposed on Monday before Tuesday's explosion damaged the pressure vessel around the reactor.

Yukiya Amano, director general of the IAEA, told a press conference there was a "possibility of core damage" at No 2 reactor, adding: "The damage is estimated to be less than 5%."

The government ordered any inhabitants remaining within the 12-mile (20km) exclusion zone to leave immediately, and told those between 12 and 19 miles away to stay indoors, while imposing a 19-mile no-fly zone. Experts backed their assessment that health risks beyond that area were minimal at present.

The news was a fresh blow for a region already reeling from the impact of Friday's magnitude 8.9 earthquake and devastating tsunami.

At midday Tuesday, Japan's national police agency said 2,475 people were confirmed dead and 3,611 were missing, while NHK television reported 3,000 dead with 15,000 unaccounted for. Emergency broadcasts on NHK underlined the danger that was unfolding at Fukushima.

"For those in the evacuation area, close your windows and doors. Switch off your air conditioners. If you are being evacuated, cover yourself as much as possible and wear a facemask. Stay calm."

The announcement came as another powerful aftershock of magnitude 6.2 was recorded near Shizuoka, south-west of Tokyo.

Survivors also face growing fears of widespread contamination. Water, food and fuel are in short supply in Ishinomaki, one of the cities worst hit. According to the deputy mayor, Etsuro Kitamura, 40,000 refugees in evacuation centres are having to live on just one rice ball a day.

For Hiroko Kodo, news of the explosion was a rude return to the world of mass communication. Since Friday she had been cut off from television, the internet, and mobile phone networks. But the Red Cross provided her with a radio in an emergency kit it distributed to all the refugees. "When I turned it on, I heard about the radiation. It is terrifying. I'm afraid now to drink the water from the mountains in case it is contaminated."

Workers at the Fukushima plant have been struggling since Friday to avert a disaster after cooling systems failed in the aftermath of the quake. Hundreds of thousands of people have already been evacuated from areas within 12 miles of the facility as a precaution.

Readings in parts of the facility hit levels indicating an immediate risk of damage to people without protective gear, Edano said.

The prime minister, Naoto Kan, asked people to remain calm in a televised address, but warned: "Radiation has spread from these reactors and the reading of the level seems high ... There's still a very high risk of further radioactive material coming out." He added that workers were "putting themselves in a very dangerous situation" to try to contain the problems.

With confidence diminishing in the ability of the plant owner, the Tokyo Electric Power Company (Tepco), to handle the crisis, Kan had already said he would personally lead a new joint response headquarters.

According to Kyodo, the prime minister called executives at the power company to demand "what the hell is going on?"

Tokyo has asked the UN nuclear watchdog for expert help and the US nuclear regulatory commission for equipment. Officials have also begun to distribute potassium iodide, which can help inhibit the uptake of radioactive iodide by the thyroid, to evacuation centres.

Edano told reporters that workers were continuing to inject water to cool units 1 to 3. The No 2 reactor was not as stable as the others, but the water injection was working "to a certain level", he added.

Tepco admitted for the first time that there was a possibility of partial meltdown, Kyodo reported. Officials have already gauged that as a "high possibility".

Edano told reporters that beyond the 12-mile radius the level should be reduced to one where harm to human health would be minimal or non-existent, although that would depend on wind speed and direction. He said a "minimal amount" of radioactive material might spread to metropolitan areas, but not at harmful levels, adding: "We want you to keep calm. We can continue with our daily lives."

In Tokyo, the metropolitan government said radiation reached around 20 times normal levels in the capital on Tuesday morning but said governor Shintaro Ishihara said the levels would "not immediately cause health problems".

Prof David Hinde, head of the department of nuclear physics at the Australian National University, said it was the worst nuclear accident since the Chernobyl disaster in 1986, but stressed it was on a far smaller scale.

The maximum radiation level was "very, very serious" for workers on site, who would only be able to remain there for the briefest periods. But the risk to those outside the exclusion zone was very small, particularly when seen in the context of their situation as a whole.

"Compared to the risk of being on a plain near the sea it's negligible ... no one is looking at the black smoke from the fires and wondering where those carcinogens are going," he said.

An expert told the broadcaster NHK that the situation was "very grave", warning that without protective gear a level of 100mSv could be enough to cause male infertility in a short time.

He also said those in the 12-mile to 19-mile zone should dust off their hair and clothes before entering their building, including brushing off the soles of their shoes. Once inside they should close windows and turn off air conditioning. Any laundry hanging out should be left outside.